Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008056.1 Hibiscus syriacus cultivar Beakdansim tig00110551_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2370532
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 13
Found at i:2076200 original size:19 final size:19
Alignment explanation
Indices: 2076176--2076227 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
2076166 GAAAATATTC
2076176 AGAGTGCATCGATGTATGG
1 AGAGTGCATCGATGTATGG
* *
2076195 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGTATGG
2076214 A-A-TGCATTCGATGT
1 AGAGTGCA-TCGATGT
2076228 TCAATTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 18 0.64
ACGTcount: A:0.25, C:0.13, G:0.35, T:0.27
Consensus pattern (19 bp):
AGAGTGCATCGATGTATGG
Found at i:2076268 original size:65 final size:64
Alignment explanation
Indices: 2076070--2076276 Score: 217
Period size: 65 Copynumber: 3.2 Consensus size: 64
2076060 GCACCAAGTG
* * * **
2076070 TGCATCGGTGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATGTCTTG-
1 TGCATCGGTGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGGATTGA
* * *
2076134 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGTATGGA--
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCATGGATT
2076196 GA
63 GA
* * *
2076198 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGGATT
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATGGATT
2076262 GA
63 GA
2076264 TGCATCGGTGCAT
1 TGCATCGGTGCAT
2076277 ACCTTTGAAT
Statistics
Matches: 119, Mismatches: 14, Indels: 19
0.78 0.09 0.12
Matches are distributed among these distances:
63 10 0.08
64 43 0.36
65 62 0.52
66 4 0.03
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (64 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGGATTGA
Found at i:2076643 original size:31 final size:31
Alignment explanation
Indices: 2076605--2076684 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
2076595 ATCGATTTTG
*
2076605 AAAAACTTACTCCCTCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
2076636 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACTCCCCCTTACTATAGCACATC
** * *
2076667 TTAAATTTTCTCCCCCTT
1 AAAAACTTACTCCCCCTT
2076685 TTTGTTAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.31, C:0.34, G:0.03, T:0.33
Consensus pattern (31 bp):
AAAAACTTACTCCCCCTTACTATAGCACATC
Found at i:2081693 original size:20 final size:21
Alignment explanation
Indices: 2081654--2081700 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2081644 GAGTTTGTTT
2081654 TCATTTTTCAATTTTGAAAAA
1 TCATTTTTCAATTTTGAAAAA
2081675 TCATTTTT-ATATTTT-AAAAA
1 TCATTTTTCA-ATTTTGAAAAA
*
2081695 TAATTT
1 TCATTT
2081701 CTCATAATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAAAA
Found at i:2083755 original size:19 final size:19
Alignment explanation
Indices: 2083731--2083781 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2083721 GAAAATATTC
2083731 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
2083750 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
2083769 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
2083782 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:2083823 original size:65 final size:64
Alignment explanation
Indices: 2083625--2083831 Score: 219
Period size: 65 Copynumber: 3.2 Consensus size: 64
2083615 GCACCAAGTG
* * * *
2083625 TGCATCGGTGCATGAAATGCATTCGATGTTTGAAAAATAGCATGGTGCATTGATGCAT-GTCTTG
1 TGCATCGGTGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGGAC-TG
2083689 -
64 A
* *
2083689 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCATGGACT
2083751 GA
63 GA
* * *
2083753 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGGACT
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATGGACT
2083817 GA
63 GA
2083819 TGCATCGGTGCAT
1 TGCATCGGTGCAT
2083832 ACCTTTGAAT
Statistics
Matches: 121, Mismatches: 11, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
63 10 0.08
64 44 0.36
65 62 0.51
66 5 0.04
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (64 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGGACTGA
Found at i:2088627 original size:19 final size:19
Alignment explanation
Indices: 2088603--2088653 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
2088593 GGAACACTTA
*
2088603 GTGCATCGGTGCACCAAGT
1 GTGCATCGATGCACCAAGT
2088622 GTGCATCGATGCACCAAGT
1 GTGCATCGATGCACCAAGT
*
2088641 GTGTATCGATGCA
1 GTGCATCGATGCA
2088654 TAAAATGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (19 bp):
GTGCATCGATGCACCAAGT
Found at i:2088724 original size:64 final size:64
Alignment explanation
Indices: 2088622--2088799 Score: 198
Period size: 64 Copynumber: 2.8 Consensus size: 64
2088612 TGCACCAAGT
* * * * **
2088622 GTGCATCGATGCACCA-AGTGTGTATCGATGCATAAAATGCATTCGATGTTTGAA-AATAACCTG
1 GTGCATCGATGCA-TAGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAA-AACCCA
2088685 A
64 A
* *** * * *
2088686 GTGCATCGATGCATTGCTTGTGCATTGATGCATGAAATGCATTCTATGTTTTAATAAAACCCAA
1 GTGCATCGATGCATAGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCAA
*
2088750 GTGTATCGATGCATAGAGAGTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATAGAGAGTGCATCGATGCATGAAATGCATTCGATGTT
2088800 CAATTTATTC
Statistics
Matches: 94, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
64 92 0.98
65 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATAGAGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCAA
Found at i:2090967 original size:219 final size:219
Alignment explanation
Indices: 2090588--2091018 Score: 709
Period size: 219 Copynumber: 2.0 Consensus size: 219
2090578 CCACCCTAGT
2090588 GGTGGTGGTGCAGGATTCACCCATAACAGAGGTGAGACTGGTGGCTATGGAGGAGACGGCGTACA
1 GGTGGTGGTGCAGGATTCACCCATAACAGAGGTGAGACTGGTGGCTATGGAGGAGACGGCGTACA
* * * *
2090653 TGACGCCAGCCGTGGGTACCCCACAGAAGATATTGGGACTGGGTATTACTCGGGTAGGCAGGTTA
66 TGACGCCAGCAGTGGGTACCCCACAGAAGATACTGGGACTGGGTATGACTCGGGAAGGCAGGTTA
*
2090718 GGGCGGATGAAAATATGAATATGGGGTATGGTGGAGAAACAGGGGGTGGATTAGGTTATTCAACA
131 GGGCGGATGAAAATATGAATATGGGGTATGGTGGAGAAACAGAGGGTGGATTAGGTTATTCAACA
*
2090783 ACTGGGGGAAACATTGGAGGGGCA
196 ACCGGGGGAAACATTGGAGGGGCA
* * * *
2090807 GGTGGTGGTGCTGGATTCACCCATAACAGAGGTGAGACTGGTGGCTATGGAGGCGGCGGCGTATA
1 GGTGGTGGTGCAGGATTCACCCATAACAGAGGTGAGACTGGTGGCTATGGAGGAGACGGCGTACA
* * *
2090872 TGACGCCAGCAGTGGGTACTCCACAGCAGATACTGGGACTGGGTATGACTTGGGAAGGCAGGTTA
66 TGACGCCAGCAGTGGGTACCCCACAGAAGATACTGGGACTGGGTATGACTCGGGAAGGCAGGTTA
* * *
2090937 GGTCGGATGAAAATATGAATATGGGGTATGGTGGAGACACAGAGGGTGGATTGGGTTATTCAACA
131 GGGCGGATGAAAATATGAATATGGGGTATGGTGGAGAAACAGAGGGTGGATTAGGTTATTCAACA
*
2091002 ACCGGGGGAAGCATTGG
196 ACCGGGGGAAACATTGG
2091019 TGGGACATGG
Statistics
Matches: 195, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
219 195 1.00
ACGTcount: A:0.26, C:0.15, G:0.39, T:0.21
Consensus pattern (219 bp):
GGTGGTGGTGCAGGATTCACCCATAACAGAGGTGAGACTGGTGGCTATGGAGGAGACGGCGTACA
TGACGCCAGCAGTGGGTACCCCACAGAAGATACTGGGACTGGGTATGACTCGGGAAGGCAGGTTA
GGGCGGATGAAAATATGAATATGGGGTATGGTGGAGAAACAGAGGGTGGATTAGGTTATTCAACA
ACCGGGGGAAACATTGGAGGGGCA
Found at i:2091573 original size:75 final size:74
Alignment explanation
Indices: 2091462--2091631 Score: 238
Period size: 75 Copynumber: 2.3 Consensus size: 74
2091452 AAAACAATTT
*
2091462 TTTTAGTTTTATAATT--AAAAAATACGAAAATCAATTTTAGT-TTCATAATTGAAAAAAATACT
1 TTTTAGTGTTATAATTGAAAAAAATACGAAAATCAATTTTAGTGTT-ATAATTGAAAAAAATACT
2091524 AAAATAAAAA
65 AAAATAAAAA
* * *
2091534 TATTTAGTGTTATAATTGAAAAAAATATGAAAATTAATTTTAGTGTTATAATTGAAAAAATTACT
1 T-TTTAGTGTTATAATTGAAAAAAATACGAAAATCAATTTTAGTGTTATAATTGAAAAAAATACT
*
2091599 AAAATCAAAA
65 AAAATAAAAA
* *
2091609 TTTTATTGTTCTAATTGAAAAAA
1 TTTTAGTGTTATAATTGAAAAAA
2091632 TTGAAAGTTT
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
72 1 0.01
73 14 0.16
74 20 0.23
75 50 0.57
76 2 0.02
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (74 bp):
TTTTAGTGTTATAATTGAAAAAAATACGAAAATCAATTTTAGTGTTATAATTGAAAAAAATACTA
AAATAAAAA
Found at i:2091633 original size:38 final size:37
Alignment explanation
Indices: 2091462--2091631 Score: 190
Period size: 36 Copynumber: 4.6 Consensus size: 37
2091452 AAAACAATTT
* *
2091462 TTTTAGTTTTATAATT--AAAAAATACGAAAATC-AA
1 TTTTAGTGTTATAATTGAAAAAAATACTAAAATCAAA
*
2091496 TTTTAGT-TTCATAATTGAAAAAAATACTAAAATAAAAA
1 TTTTAGTGTT-ATAATTGAAAAAAATACTAAAAT-CAAA
*
2091534 TATTTAGTGTTATAATTGAAAAAAATA-TGAAAAT-TAA
1 T-TTTAGTGTTATAATTGAAAAAAATACT-AAAATCAAA
*
2091571 TTTTAGTGTTATAATTGAAAAAATTACTAAAATCAAAA
1 TTTTAGTGTTATAATTGAAAAAAATACTAAAATC-AAA
* *
2091609 TTTTATTGTTCTAATTGAAAAAA
1 TTTTAGTGTTATAATTGAAAAAA
2091632 TTGAAAGTTT
Statistics
Matches: 118, Mismatches: 7, Indels: 18
0.83 0.05 0.13
Matches are distributed among these distances:
33 2 0.02
34 13 0.11
36 43 0.36
37 4 0.03
38 27 0.23
39 27 0.23
40 2 0.02
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (37 bp):
TTTTAGTGTTATAATTGAAAAAAATACTAAAATCAAA
Found at i:2092074 original size:17 final size:15
Alignment explanation
Indices: 2092052--2092099 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 15
2092042 CAACCATCGA
2092052 TATTTTTTTAGTCTTTT
1 TATTTTTTTA-T-TTTT
2092069 TATTTTTTCTTATTTTT
1 TA-TTTTT-TTATTTTT
2092086 TA-TTTTTTATTTTT
1 TATTTTTTTATTTTT
2092100 AATAAGCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 8 0.28
15 4 0.14
17 8 0.28
18 6 0.21
19 3 0.10
ACGTcount: A:0.12, C:0.04, G:0.02, T:0.81
Consensus pattern (15 bp):
TATTTTTTTATTTTT
Found at i:2092641 original size:2 final size:2
Alignment explanation
Indices: 2092636--2092671 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2092626 ACATAGTGTG
2092636 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2092672 ACTAGTGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2096975 original size:20 final size:20
Alignment explanation
Indices: 2096950--2097007 Score: 116
Period size: 20 Copynumber: 2.9 Consensus size: 20
2096940 CACATGTTAA
2096950 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
2096970 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
2096990 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
2097008 TCAAGGGGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:2097492 original size:15 final size:15
Alignment explanation
Indices: 2097457--2097493 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
2097447 ACAAGTGATA
2097457 TGAAAATGTATATAG
1 TGAAAATGTATATAG
2097472 TG-AAATG-ATATAAG
1 TGAAAATGTATAT-AG
2097486 TGAAAATG
1 TGAAAATG
2097494 CCCATGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.20
14 9 0.45
15 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.30
Consensus pattern (15 bp):
TGAAAATGTATATAG
Found at i:2100321 original size:20 final size:22
Alignment explanation
Indices: 2100272--2100329 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
2100262 AATTGGGTAG
2100272 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
*
2100296 TGCATCGATGCACTG-T-AGAT
1 TGCATCGATGCACTGTTAAGAA
2100316 TGCATCGATGCACT
1 TGCATCGATGCACT
2100330 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:2100815 original size:15 final size:15
Alignment explanation
Indices: 2100780--2100816 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
2100770 ACAAGTGATA
2100780 TGAAAATGTATATAG
1 TGAAAATGTATATAG
2100795 TG-AAATG-ATATAAG
1 TGAAAATGTATAT-AG
2100809 TGAAAATG
1 TGAAAATG
2100817 CGCATGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.20
14 9 0.45
15 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.30
Consensus pattern (15 bp):
TGAAAATGTATATAG
Found at i:2102743 original size:34 final size:33
Alignment explanation
Indices: 2102705--2102808 Score: 106
Period size: 34 Copynumber: 3.2 Consensus size: 33
2102695 AGAACATTTC
2102705 CATTTCATATCAAACTTGTACCTTTCACTTTATT
1 CATTTCATATCAAAC-TGTACCTTTCACTTTATT
* * *
2102739 CATTTCATAGC--A-TGTATCATTCACTTTATT
1 CATTTCATATCAAACTGTACCTTTCACTTTATT
* * *
2102769 CATTTCACATCAAACATGTGCCTTTCATTTTATT
1 CATTTCATATCAAAC-TGTACCTTTCACTTTATT
*
2102803 CTTTTC
1 CATTTC
2102809 CTAGCCCATT
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
30 25 0.45
32 2 0.04
34 29 0.52
ACGTcount: A:0.25, C:0.23, G:0.05, T:0.47
Consensus pattern (33 bp):
CATTTCATATCAAACTGTACCTTTCACTTTATT
Found at i:2102976 original size:48 final size:48
Alignment explanation
Indices: 2102922--2103128 Score: 243
Period size: 48 Copynumber: 4.3 Consensus size: 48
2102912 AATTGAAAGT
* * * *
2102922 AGCACCACCTTCACACATACGTCAGATGTGCTAGTTATCATTAATAGC
1 AGCACCACCGTCACACAGACGTCAGACGTGCTAATTATCATTAATAGC
* * * * * * * *
2102970 ATCACCATCATCACACAGATGCCAGACGTGCTAGTTATCGTTAATAGT
1 AGCACCACCGTCACACAGACGTCAGACGTGCTAATTATCATTAATAGC
** *
2103018 AGCACCATAGTCACACAGACGTCAAACGTGCTAATTATCATTAATAGC
1 AGCACCACCGTCACACAGACGTCAGACGTGCTAATTATCATTAATAGC
* * * *
2103066 AGCACCACCGTTACACAGACGTCAGACGTGCTAATTATCTTTGATAGT
1 AGCACCACCGTCACACAGACGTCAGACGTGCTAATTATCATTAATAGC
2103114 AGCACCACCGTCACA
1 AGCACCACCGTCACA
2103129 AAAGTGACAT
Statistics
Matches: 133, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 133 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (48 bp):
AGCACCACCGTCACACAGACGTCAGACGTGCTAATTATCATTAATAGC
Found at i:2103127 original size:96 final size:96
Alignment explanation
Indices: 2102914--2103128 Score: 277
Period size: 96 Copynumber: 2.2 Consensus size: 96
2102904 CTAGGTACAA
* * * * * * * *
2102914 TTGAAAGTAGCACCACCTTCACACATACGTCAGATGTGCTAGTTATCATTAATAGCATCACCATC
1 TTGATAGTAGCACCACCGTCACACAGACGTCAAACGTGCTAATTATCATTAATAGCAGCACCACC
* *
2102979 ATCACACAGATGCCAGACGTGCTAGTTATCG
66 ATCACACAGACGCCAGACGTGCTAATTATCG
* **
2103010 TTAATAGTAGCACCATAGTCACACAGACGTCAAACGTGCTAATTATCATTAATAGCAGCACCACC
1 TTGATAGTAGCACCACCGTCACACAGACGTCAAACGTGCTAATTATCATTAATAGCAGCACCACC
* * * *
2103075 GTTACACAGACGTCAGACGTGCTAATTATCT
66 ATCACACAGACGCCAGACGTGCTAATTATCG
2103106 TTGATAGTAGCACCACCGTCACA
1 TTGATAGTAGCACCACCGTCACA
2103129 AAAGTGACAT
Statistics
Matches: 99, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
96 99 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (96 bp):
TTGATAGTAGCACCACCGTCACACAGACGTCAAACGTGCTAATTATCATTAATAGCAGCACCACC
ATCACACAGACGCCAGACGTGCTAATTATCG
Found at i:2105963 original size:118 final size:118
Alignment explanation
Indices: 2105703--2105967 Score: 356
Period size: 118 Copynumber: 2.2 Consensus size: 118
2105693 AAAATATATA
* * * *
2105703 GACGATAACATAACCGGTTAATTATTGGAAACATTATCAAGCACAATAACATATTAGGTAGCACT
1 GACGATAACAAAACAGGTTAATTACTGGAAACATTATCAAGCACAATAACATATTAGATAGCACT
*
2105768 TATATAACATAATAGGTAGCGCCTTGTTAAAGCTGATGGAGCTTTGGAAATCC
66 TATATAACATAATAGGTAGCACCTTGTTAAAGCTGATGGAGCTTTGGAAATCC
* * * *
2105821 GAGGAAAACATAACCA-GTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGATAGCAC
1 GACGATAACA-AAACAGGTTAATTACTGGAAACATTATCAAGCACAATAACATATTAGATAGCAC
* * * *
2105885 TTATATAATATAATAGGTAGCACCTT-TTTAAGC-GATGGGGCTTTTGGAAATCT
65 TTATATAACATAATAGGTAGCACCTTGTTAAAGCTGATGGAGC-TTTGGAAATCC
*
2105938 GACGATAACAAAATAGGTTATATTACTGGA
1 GACGATAACAAAACAGGTTA-ATTACTGGA
2105968 TTTGTTATTA
Statistics
Matches: 126, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
116 10 0.08
117 28 0.22
118 86 0.68
119 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (118 bp):
GACGATAACAAAACAGGTTAATTACTGGAAACATTATCAAGCACAATAACATATTAGATAGCACT
TATATAACATAATAGGTAGCACCTTGTTAAAGCTGATGGAGCTTTGGAAATCC
Found at i:2106747 original size:19 final size:19
Alignment explanation
Indices: 2106725--2106762 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2106715 ATCGATTGTT
* *
2106725 TAAAATTTTTACCGTTTTC
1 TAAAATTTTAACCGGTTTC
2106744 TAAAATTTTAACCGGTTTC
1 TAAAATTTTAACCGGTTTC
2106763 GACAACAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (19 bp):
TAAAATTTTAACCGGTTTC
Found at i:2108884 original size:66 final size:62
Alignment explanation
Indices: 2108744--2108910 Score: 165
Period size: 66 Copynumber: 2.5 Consensus size: 62
2108734 TCTGGACAAG
* * * * **
2108744 GTGCATCGATGCACATTCATAAGTGCATCGATGCATTCCTTTAAAAGAAGAACATCGAATGCCTT
1 GTGCATCGATGCATA-GC-TAA-TGCATCGATGCA-TCCTTTAAAAAAAGAACATCAAATGCAGT
*
2108809 T
62 A
2108810 GATGCATCGATGCATAGCTAATGCATCGATGCATCCTTTTAAAATAATAGAACATCAAATGCAAG
1 G-TGCATCGATGCATAGCTAATGCATCGATGCATCC-TTTAAAA-AA-AGAACATCAAATGC-AG
2108875 TA
61 TA
*
2108877 GTGCATCGATGCATAAGGT-ATGCATCGATGCATC
1 GTGCATCGATGCAT-AGCTAATGCATCGATGCATC
2108911 TCATTAATAA
Statistics
Matches: 87, Mismatches: 8, Indels: 12
0.81 0.07 0.11
Matches are distributed among these distances:
63 3 0.03
64 19 0.22
65 4 0.05
66 43 0.49
67 18 0.21
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (62 bp):
GTGCATCGATGCATAGCTAATGCATCGATGCATCCTTTAAAAAAAGAACATCAAATGCAGTA
Found at i:2109687 original size:30 final size:30
Alignment explanation
Indices: 2109651--2109714 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
2109641 AAGGAACATA
* *
2109651 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
2109681 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
2109711 TGGA
1 TGGA
2109715 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:2112653 original size:19 final size:20
Alignment explanation
Indices: 2112607--2112653 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
2112597 ATTTGTTATA
*
2112607 TTTAATCGTTTGTTTAAATT
1 TTTAACCGTTTGTTTAAATT
*
2112627 TTTTACCGTTT-TCTTAAA-T
1 TTTAACCGTTTGT-TTAAATT
2112646 TTTAACCG
1 TTTAACCG
2112654 ATTTAGAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTAACCGTTTGTTTAAATT
Found at i:2114003 original size:6 final size:6
Alignment explanation
Indices: 2113992--2114030 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
2113982 ATTTATATTG
* * *
2113992 AAATTC AAATTC AAACTC AAATTG AAATTT AAATTC AAA
1 AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAA
2114031 CTCCAATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.31
Consensus pattern (6 bp):
AAATTC
Found at i:2114011 original size:12 final size:12
Alignment explanation
Indices: 2113996--2114038 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
2113986 ATATTGAAAT
2113996 TCAAATTCAAAC
1 TCAAATTCAAAC
* *
2114008 TCAAATTGAAAT
1 TCAAATTCAAAC
*
2114020 TTAAATTCAAAC
1 TCAAATTCAAAC
*
2114032 TCCAATT
1 TCAAATT
2114039 AAAAATGAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.33
Consensus pattern (12 bp):
TCAAATTCAAAC
Found at i:2114015 original size:24 final size:24
Alignment explanation
Indices: 2113988--2114038 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
2113978 CAAAATTTAT
2113988 ATTGAAATTCAAATTCAAACTCAA
1 ATTGAAATTCAAATTCAAACTCAA
* *
2114012 ATTGAAATTTAAATTCAAACTCCA
1 ATTGAAATTCAAATTCAAACTCAA
2114036 ATT
1 ATT
2114039 AAAAATGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (24 bp):
ATTGAAATTCAAATTCAAACTCAA
Found at i:2114049 original size:24 final size:24
Alignment explanation
Indices: 2113998--2114049 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2113988 ATTGAAATTC
* * *
2113998 AAATTCAAACTCAAATTGAAATTT
1 AAATTCAAACTCAAATTAAAAATG
*
2114022 AAATTCAAACTCCAATTAAAAATG
1 AAATTCAAACTCAAATTAAAAATG
2114046 AAAT
1 AAAT
2114050 GAACATGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.13, G:0.04, T:0.29
Consensus pattern (24 bp):
AAATTCAAACTCAAATTAAAAATG
Found at i:2116611 original size:18 final size:17
Alignment explanation
Indices: 2116590--2116667 Score: 79
Period size: 18 Copynumber: 4.4 Consensus size: 17
2116580 TGATTTGGTC
2116590 AGAAGAAGAGATTGGTTG
1 AGAAGAAGAG-TTGGTTG
*
2116608 AGAAGAAG-GTTGTCGTTA
1 AGAAGAAGAGTTG--GTTG
2116626 AGAAGAAGAGCTTGGTTG
1 AGAAGAAGAG-TTGGTTG
2116644 AGAAGAAG-GTTGTCGTTG
1 AGAAGAAGAGTTG--GTTG
2116662 AGAAGA
1 AGAAGA
2116668 CCCGCACCTC
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
16 6 0.12
17 2 0.04
18 40 0.77
19 1 0.02
20 3 0.06
ACGTcount: A:0.36, C:0.04, G:0.37, T:0.23
Consensus pattern (17 bp):
AGAAGAAGAGTTGGTTG
Found at i:2116641 original size:36 final size:36
Alignment explanation
Indices: 2116590--2116667 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
2116580 TGATTTGGTC
2116590 AGAAGAAGAGATTGGTTGAGAAGAAGGTTGTCGTTA
1 AGAAGAAGAGATTGGTTGAGAAGAAGGTTGTCGTTA
* *
2116626 AGAAGAAGAGCTTGGTTGAGAAGAAGGTTGTCGTTG
1 AGAAGAAGAGATTGGTTGAGAAGAAGGTTGTCGTTA
2116662 AGAAGA
1 AGAAGA
2116668 CCCGCACCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.36, C:0.04, G:0.37, T:0.23
Consensus pattern (36 bp):
AGAAGAAGAGATTGGTTGAGAAGAAGGTTGTCGTTA
Found at i:2117273 original size:201 final size:200
Alignment explanation
Indices: 2116956--2118092 Score: 1742
Period size: 201 Copynumber: 5.7 Consensus size: 200
2116946 TTAAAACATT
* *
2116956 GTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGGTATATTTTTACCAGTTACATTGTA
1 GTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGATATATTTTTACCGGTTACATTGTA
*
2117021 AATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTAAGGATCGATACTTAATAAAAATGT
66 AATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGAGGATCGATACTTAATAAAAATGT
*
2117086 ATCGACACTTTATGTGTGCATCTCGTTTGGCATTCATTCTGGACAAAAAGTATCGATACAATTTA
131 ATCGACACTTTATGCGTGCATCTCGTTTGGCATTCATTCTGGACAAAAAGTATCGATACAATTTA
2117151 AAAAA
196 AAAAA
* *
2117156 GTATCGATACATTATGTTTACCTATTCTTTCATTAAACCAATATATTTTTACCGGTTACATTGTA
1 GTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGATATATTTTTACCGGTTACATTGT-
* *
2117221 AAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGATGATCGATACTTAATTAAAATG
65 AAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGAGGATCGATACTTAATAAAAATG
*
2117286 TATCGACACTTTATGCGTGCATCTCGTTTGGCATTCATTCTGGATAAAAAGTATCGATACAATTT
130 TATCGACACTTTATGCGTGCATCTCGTTTGGCATTCATTCTGGACAAAAAGTATCGATACAATTT
2117351 AAAAAA
195 AAAAAA
* * *
2117357 GTATCGATACATTATGTTTACCTATTCTTTCATTAAACCAATATATTTTTACTGGTTACATTGTA
1 GTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGATATATTTTTACCGGTTACATTGT-
* *
2117422 AAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGATGATCGATACTTTATAAAAATG
65 AAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGAGGATCGATACTTAATAAAAATG
* *
2117487 TATCGACACTTTATGCGTACATCTCGTTTGGCAATCATTCTGGACAAAAAGTATCGATACAATTT
130 TATCGACACTTTATGCGTGCATCTCGTTTGGCATTCATTCTGGACAAAAAGTATCGATACAATTT
2117552 AAAAAAA
195 -AAAAAA
* * *
2117559 ATATCGATACATTATGTTTACCTTTTCT-TCCATTAAACCGGTATATTTTTACCGGTTACATTGT
1 GTATCGATACATTATGTTTACCTATTCTCT-CATTAAACCGATATATTTTTACCGGTTACATTGT
* * * ** *
2117623 AAATTTACATATTACTTTATAATAATAGGTTTTGACATTTTGAGGATCGATACTTTATAAAAATG
65 AAATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGAGGATCGATACTTAATAAAAATG
* * * *
2117688 TATCAACACTTTATGCGTGCATCTCGTTTGACATTCATTCTGGACAAAAAGTTTCAATA-AATTT
130 TATCGACACTTTATGCGTGCATCTCGTTTGGCATTCATTCTGGACAAAAAGTATCGATACAA-TT
2117752 TAAAAAA
194 TAAAAAA
* * *
2117759 GTATCGATACATTATGTTTACCTATTCTCTCATTAAATCGATATATTTTTACCTGTTACATTCTA
1 GTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGATATATTTTTACCGGTTACATTGTA
* * * * *
2117824 AATTTACCTATTACTTTATAATAATCAGTTTCGATATTTTTAGGATAGATACTTAATATAAATGT
66 AATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGAGGATCGATACTTAATAAAAATGT
* * * * * * *
2117889 ATTGCCACTTTATGCATACATCTCGTTTGGAAATCATTCTGGACAAAAAGTATCAATACAATTT-
131 ATCGACACTTTATGCGTGCATCTCGTTTGGCATTCATTCTGGACAAAAAGTATCGATACAATTTA
*
2117953 AAAAT
196 AAAAA
* **
2117958 GTATCGATACATTATGTTTACCTATTCTCTCATTAAACTGATATATTTTTATAGGTTACATTGTA
1 GTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGATATATTTTTACCGGTTACATTGTA
* *
2118023 AATTTAACTATTACTTTATAATAATCAGTTTCGATGTTTTGAGGATCGATACTT-ATAATAAATG
66 AATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGAGGATCGATACTTAATAA-AAATG
2118087 TATCGA
130 TATCGA
2118093 TACCTCTAGT
Statistics
Matches: 860, Mismatches: 70, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
198 3 0.00
199 122 0.14
200 233 0.27
201 439 0.51
202 63 0.07
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.41
Consensus pattern (200 bp):
GTATCGATACATTATGTTTACCTATTCTCTCATTAAACCGATATATTTTTACCGGTTACATTGTA
AATTTACCTATTACTTTATAATAATCGGTTTCGATGTTTTGAGGATCGATACTTAATAAAAATGT
ATCGACACTTTATGCGTGCATCTCGTTTGGCATTCATTCTGGACAAAAAGTATCGATACAATTTA
AAAAA
Found at i:2122510 original size:66 final size:65
Alignment explanation
Indices: 2122432--2122556 Score: 178
Period size: 66 Copynumber: 1.9 Consensus size: 65
2122422 ACCACCCCCT
* *
2122432 TCACCTCGTAAGTTCACCCCTCAATTCCACAACTTCCTTCACCACTCAATCAATTTTTCCACCCG
1 TCACCTCGTAAGTCCACCCCTCAACTCCACAACTTCCTTCACCACTCAATCAATTTTTCCACCCG
* * * * *
2122497 TCACCATCTTAAGTCCACCCCTCAACTCCTCAACTTCTTTCACCACTCCATCTATTTTTC
1 TCACC-TCGTAAGTCCACCCCTCAACTCCACAACTTCCTTCACCACTCAATCAATTTTTC
2122557 ACACACTTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
65 5 0.10
66 47 0.90
ACGTcount: A:0.23, C:0.42, G:0.03, T:0.32
Consensus pattern (65 bp):
TCACCTCGTAAGTCCACCCCTCAACTCCACAACTTCCTTCACCACTCAATCAATTTTTCCACCCG
Found at i:2123026 original size:24 final size:25
Alignment explanation
Indices: 2122984--2123033 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
2122974 ACCTGCATTT
2122984 ATAATTAAATTTATCATTTTATATA
1 ATAATTAAATTTATCATTTTATATA
* *
2123009 ATAATTATA-TTATTATTTTATATA
1 ATAATTAAATTTATCATTTTATATA
2123033 A
1 A
2123034 AAAACAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
ATAATTAAATTTATCATTTTATATA
Found at i:2124889 original size:23 final size:25
Alignment explanation
Indices: 2124841--2124889 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 25
2124831 TTAGCTACGC
*
2124841 ATTTGATATTTTAATCGGATATATT
1 ATTTGATATTTTAATCGGATAAATT
2124866 ATTT-ATA-TTTAATC-GATACAATT
1 ATTTGATATTTTAATCGGATA-AATT
2124889 A
1 A
2124890 CTAAGTCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 4 0.18
23 11 0.50
24 3 0.14
25 4 0.18
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.49
Consensus pattern (25 bp):
ATTTGATATTTTAATCGGATAAATT
Found at i:2125280 original size:183 final size:182
Alignment explanation
Indices: 2125019--2125459 Score: 650
Period size: 183 Copynumber: 2.4 Consensus size: 182
2125009 TCCGGTATCA
* * * * *
2125019 CTTTACCGGTTTTTTCATAATGAAA-CTTTTTATCATACTTTTACCTGTTATGTTGTTACATATC
1 CTTTACCGGTTTTGTCATAATGAAACCGTTTTGTCATATTTTTACCTGTTATATTGTTACATATC
* *
2125083 GATACATATTTATAAAGTATCGATACTTTATAGGCGCTATTAATGATTTTCTTTAAAATTCTATA
66 GATACATATTTATAAAGTATCGATACTTTATAGGCGCTATTAATGATTTTCTTTAAAAATCCATA
* * *
2125148 AGTATCGATACTTATTTGAATGGAATCGATACCTTCAACATATCTACTAGTG
131 AGTATCGATACTTATTTGAATGGAATCGATACATTCAACATATCCACTAGCG
2125200 CTTTACCGGTTTTGTCATAATGAAACCGGTTTTGTCATATTTTTACCTGTTATATTGTTACATAT
1 CTTTACCGGTTTTGTCATAATGAAACC-GTTTTGTCATATTTTTACCTGTTATATTGTTACATAT
* * *
2125265 CGATACATGTTTATAAAGTATCGATACTTTATAGGCTCTATTAATGCTTTTCTTTAAAAATCCAT
65 CGATACATATTTATAAAGTATCGATACTTTATAGGCGCTATTAATGATTTTCTTTAAAAATCCAT
* **
2125330 AAGTATCGATACTTATTTGAATGTAATCGATACATTCAACATATCCGGTAGCG
130 AAGTATCGATACTTATTTGAATGGAATCGATACATTCAACATATCCACTAGCG
* * * * * **
2125383 CTTTACCAGTTTTGTCATATTGAACCCAGTTATGTCATATTTTTACCTGATATATTGTTATGTAT
1 CTTTACCGGTTTTGTCATAATGAAACC-GTTTTGTCATATTTTTACCTGTTATATTGTTACATAT
2125448 CGATACATATTT
65 CGATACATATTT
2125460 GAATGGTATC
Statistics
Matches: 233, Mismatches: 25, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
181 24 0.10
182 1 0.00
183 208 0.89
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.43
Consensus pattern (182 bp):
CTTTACCGGTTTTGTCATAATGAAACCGTTTTGTCATATTTTTACCTGTTATATTGTTACATATC
GATACATATTTATAAAGTATCGATACTTTATAGGCGCTATTAATGATTTTCTTTAAAAATCCATA
AGTATCGATACTTATTTGAATGGAATCGATACATTCAACATATCCACTAGCG
Found at i:2126867 original size:18 final size:18
Alignment explanation
Indices: 2126835--2126878 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
2126825 GGGTGCGTTT
2126835 AGGATAGGT-TAGGTT-AG
1 AGGAT-GGTGTAGGTTAAG
2126852 AGGTATGGTGTAGGTTAAG
1 AGG-ATGGTGTAGGTTAAG
2126871 AGGATGGT
1 AGGATGGT
2126879 ACTAGGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 6 0.25
18 13 0.54
19 5 0.21
ACGTcount: A:0.27, C:0.00, G:0.43, T:0.30
Consensus pattern (18 bp):
AGGATGGTGTAGGTTAAG
Found at i:2126884 original size:19 final size:18
Alignment explanation
Indices: 2126844--2126886 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
2126834 TAGGATAGGT
*
2126844 TAGGTTAGAGGTATGGTG
1 TAGGTTAGAGGTATGGTC
2126862 TAGGTTAAGAGG-ATGGTAC
1 TAGGTT-AGAGGTATGGT-C
2126881 TAGGTT
1 TAGGTT
2126887 TTCAGTCGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.26, C:0.02, G:0.40, T:0.33
Consensus pattern (18 bp):
TAGGTTAGAGGTATGGTC
Found at i:2132745 original size:22 final size:22
Alignment explanation
Indices: 2132713--2132762 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
2132703 AAGATAAATT
*
2132713 ATTTATTTAATCATATAATTATC
1 ATTT-TTTAATCACATAATTATC
* *
2132736 TTTTTTTAATTACATAATTATC
1 ATTTTTTAATCACATAATTATC
2132758 ATTTT
1 ATTTT
2132763 AGTTTTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTTTTAATCACATAATTATC
Found at i:2135549 original size:3 final size:3
Alignment explanation
Indices: 2135541--2135566 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2135531 TCCCAAATCA
2135541 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2135567 ATCAGTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2136675 original size:15 final size:16
Alignment explanation
Indices: 2136642--2136676 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2136632 CTCAAGCAAA
2136642 AAAAGCTCAGCTCAAC
1 AAAAGCTCAGCTCAAC
*
2136658 AAAAGCTTAGCT-AAC
1 AAAAGCTCAGCTCAAC
2136673 AAAA
1 AAAA
2136677 TTCTAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.51, C:0.23, G:0.11, T:0.14
Consensus pattern (16 bp):
AAAAGCTCAGCTCAAC
Found at i:2138759 original size:30 final size:30
Alignment explanation
Indices: 2138723--2138781 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
2138713 ACCACATAGA
*
2138723 ACATCCCATGATAATAACTAGTCTTCTGAT
1 ACATCCCATGATAATAACTAGTATTCTGAT
2138753 ACATCCCATGATAATAACTAGTATTCTGA
1 ACATCCCATGATAATAACTAGTATTCTGA
2138782 AGCTTTTGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.32
Consensus pattern (30 bp):
ACATCCCATGATAATAACTAGTATTCTGAT
Found at i:2140038 original size:105 final size:105
Alignment explanation
Indices: 2139856--2140063 Score: 407
Period size: 105 Copynumber: 2.0 Consensus size: 105
2139846 AATGCAACGC
2139856 TATGTAATTCATATTTCAAAGGCAACTTTTAATTTTCGGTTCGAAGCAAAGCCAATTTAAAGGAT
1 TATGTAATTCATATTTCAAAGGCAACTTTTAATTTTCGGTTCGAAGCAAAGCCAATTTAAAGGAT
*
2139921 CATTCTCTTGTTTTTGGAACATGTTTGATTGGTTTTTTTT
66 CATTCTCTTGTTTTTGGAACATGTTTGATAGGTTTTTTTT
2139961 TATGTAATTCATATTTCAAAGGCAACTTTTAATTTTCGGTTCGAAGCAAAGCCAATTTAAAGGAT
1 TATGTAATTCATATTTCAAAGGCAACTTTTAATTTTCGGTTCGAAGCAAAGCCAATTTAAAGGAT
2140026 CATTCTCTTGTTTTTGGAACATGTTTGATAGGTTTTTT
66 CATTCTCTTGTTTTTGGAACATGTTTGATAGGTTTTTT
2140064 AAAAAAAATT
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 102 1.00
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.44
Consensus pattern (105 bp):
TATGTAATTCATATTTCAAAGGCAACTTTTAATTTTCGGTTCGAAGCAAAGCCAATTTAAAGGAT
CATTCTCTTGTTTTTGGAACATGTTTGATAGGTTTTTTTT
Found at i:2140326 original size:132 final size:132
Alignment explanation
Indices: 2140089--2140353 Score: 442
Period size: 132 Copynumber: 2.0 Consensus size: 132
2140079 ACAAGGTAAT
*
2140089 AAAAAATTGAAAATAAGATACAAATGATTTTTCAATTACAAAGTGTTGTTTTGCTGAGTCTTTCA
1 AAAAAATTGAAAATAAGATACAAATGATTTTTCAATTACAAAGTGTTGTTTTGCTGAATCTTTCA
* *
2140154 TCGTTAAAAGTTGTAAAATGATCTCTTATTATGTGATATTATTTTATTGAGTCTCTCTGTTATTA
66 TCGTTAAAAGTTGTAAAATAATCTCTTATTATGAGATATTATTTTATTGAGTCTCTCTGTTATTA
2140219 AA
131 AA
** * * *
2140221 AAAAAATT-AGAAATATTATACAAATGGTTTTTCGATTACAAAGTGTTGTTTTGTTGAATCTTTC
1 AAAAAATTGA-AAATAAGATACAAATGATTTTTCAATTACAAAGTGTTGTTTTGCTGAATCTTTC
2140285 ATCGTTAAAAGTTGTAAAATAATCTCTTATTATGAGATATTATTTTATTGAGTCTCTCTGTTATT
65 ATCGTTAAAAGTTGTAAAATAATCTCTTATTATGAGATATTATTTTATTGAGTCTCTCTGTTATT
2140350 AAA
130 AAA
2140353 A
1 A
2140354 GTTATAAAAT
Statistics
Matches: 124, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
131 1 0.01
132 123 0.99
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (132 bp):
AAAAAATTGAAAATAAGATACAAATGATTTTTCAATTACAAAGTGTTGTTTTGCTGAATCTTTCA
TCGTTAAAAGTTGTAAAATAATCTCTTATTATGAGATATTATTTTATTGAGTCTCTCTGTTATTA
AA
Found at i:2140530 original size:28 final size:28
Alignment explanation
Indices: 2140497--2140554 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
2140487 TTAGCGCTGC
* *
2140497 TTTCAAACACTGACTTAACTACATAATG
1 TTTCAAACACTGACTCAACGACATAATG
*
2140525 TTTCAAGCACTGACTCAACGACATAATG
1 TTTCAAACACTGACTCAACGACATAATG
2140553 TT
1 TT
2140555 GATGGAGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.31
Consensus pattern (28 bp):
TTTCAAACACTGACTCAACGACATAATG
Found at i:2141670 original size:158 final size:157
Alignment explanation
Indices: 2141369--2141671 Score: 350
Period size: 158 Copynumber: 1.9 Consensus size: 157
2141359 TGATTTAGTC
* * * *
2141369 CATGATTTTCTTATTTCTTCAATTCATCGTTTATTTTAAGTGCATTTTTTACCAAATTTGAAGCA
1 CATGATTTCCTTATTTCTTCAATCCATCGTTCATTTTAAGTGCATTTTTTACCAAATTTGAACCA
* * * * * **
2141434 CATTCTCTTAAACCACCTTAGAATACCTATGTGATTTCAATTCATATTTTTGATAACATTTTGTT
66 CATGCTCTTAAACCACCTTAGAATACCTATGTAACTTCAATTCATATTTTTGATAAAATATACTT
2141499 ACTTTTTCAATTTAGCCCCTCAACTTTT
131 ACTTTTT-AATTTAGCCCCTCAACTTTT
2141527 CATGATTTCCTTATTTCTTCAATCCATTC-TTCATTTTAAGT-CTATTTTTTTACCAAATTTGAA
1 CATGATTTCCTTATTTCTTCAATCCA-TCGTTCATTTTAAGTGC-A-TTTTTTACCAAATTTGAA
* * *
2141590 CCACATGCTC-TATACCA-CTATAGAATATCTATGTAACTTCAATT-ACTATTTTTTACTAAAAA
63 CCACATGCTCTTAAACCACCT-TAGAATACCTATGTAACTTCAATTCA-TATTTTTGA-T-AAAA
2141652 TATACTCT-CTTTTT-ATTTAG
124 TATACT-TACTTTTTAATTTAG
2141672 TCCATTAACT
Statistics
Matches: 123, Mismatches: 14, Indels: 16
0.80 0.09 0.10
Matches are distributed among these distances:
157 4 0.03
158 77 0.63
159 29 0.24
160 12 0.10
161 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (157 bp):
CATGATTTCCTTATTTCTTCAATCCATCGTTCATTTTAAGTGCATTTTTTACCAAATTTGAACCA
CATGCTCTTAAACCACCTTAGAATACCTATGTAACTTCAATTCATATTTTTGATAAAATATACTT
ACTTTTTAATTTAGCCCCTCAACTTTT
Found at i:2141875 original size:2 final size:2
Alignment explanation
Indices: 2141868--2141903 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2141858 TGTGAAAAGA
2141868 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2141904 TATGGTTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2148469 original size:31 final size:31
Alignment explanation
Indices: 2148431--2148491 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
2148421 GAGTTGAGGG
*
2148431 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGA
2148462 TTACCTATGTTCTTCGGAACATATGGACTG
1 TTACCTATGTTCTTCGGAACATATGGACTG
2148492 GTCCTTCGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGA
Found at i:2149054 original size:21 final size:21
Alignment explanation
Indices: 2149028--2149067 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2149018 GAAATTACTA
*
2149028 TAGCAGTGCATCGGTACACTG
1 TAGCAGTGCATCGATACACTG
2149049 TAGCAGTGCATCGATACAC
1 TAGCAGTGCATCGATACAC
2149068 ATTTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (21 bp):
TAGCAGTGCATCGATACACTG
Found at i:2150517 original size:16 final size:16
Alignment explanation
Indices: 2150496--2150528 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2150486 TGGTGGAGTA
*
2150496 TGGCAAGCAGTTGATG
1 TGGCAAGCAGCTGATG
2150512 TGGCAAGCAGCTGATG
1 TGGCAAGCAGCTGATG
2150528 T
1 T
2150529 AGCATAGGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.15, G:0.36, T:0.24
Consensus pattern (16 bp):
TGGCAAGCAGCTGATG
Found at i:2155896 original size:51 final size:50
Alignment explanation
Indices: 2155833--2155938 Score: 110
Period size: 50 Copynumber: 2.1 Consensus size: 50
2155823 GTAGCAGTAA
** *
2155833 AGCGCGCTCCCTGCCCCGTGCTATATGCTGATTTGA-C-GCCACGTGGGGTAT
1 AGCGCGCTCCCTGCCCCGCACTATA-GCTG-TTT-ATCTGACACGTGGGGTAT
**
2155884 AGCGCGGC-CCCTGTTCCGCACTATAGCTGTTTATCTGACACGTGGGGTAT
1 AGCGC-GCTCCCTGCCCCGCACTATAGCTGTTTATCTGACACGTGGGGTAT
2155934 AGCGC
1 AGCGC
2155939 AGTACAGGGG
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
48 1 0.02
49 4 0.09
50 22 0.47
51 18 0.38
52 2 0.04
ACGTcount: A:0.15, C:0.30, G:0.29, T:0.25
Consensus pattern (50 bp):
AGCGCGCTCCCTGCCCCGCACTATAGCTGTTTATCTGACACGTGGGGTAT
Found at i:2161733 original size:14 final size:13
Alignment explanation
Indices: 2161697--2161734 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
2161687 AAACAATAAG
*
2161697 TATAAAAAAAATT
1 TATAACAAAAATT
2161710 TATAAC-AAAATT
1 TATAACAAAAATT
2161722 TATAACGAAAAAT
1 TATAAC-AAAAAT
2161735 CACACGAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 12 0.55
13 5 0.23
14 5 0.23
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (13 bp):
TATAACAAAAATT
Found at i:2162114 original size:51 final size:51
Alignment explanation
Indices: 2162011--2162125 Score: 133
Period size: 51 Copynumber: 2.3 Consensus size: 51
2162001 CCCCTACGTG
**
2162011 GCATATAGCGCGGAACAGGGGGCGCACTATACCCAAGTATAAGCCATGTCA
1 GCATATAGCGCGGAACAGGGGGCGCACTATACCCAAGTATAAGCCAAATCA
* * * ** * *
2162062 GCGTATAGCGCGGTACAGGGTGCGTGCTATACCCCATGTA-ACGCCAAATCA
1 GCATATAGCGCGGAACAGGGGGCGCACTATA-CCCAAGTATAAGCCAAATCA
2162113 GCATATAGCGCGG
1 GCATATAGCGCGG
2162126 GATAGGGAGC
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
51 46 0.87
52 7 0.13
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.17
Consensus pattern (51 bp):
GCATATAGCGCGGAACAGGGGGCGCACTATACCCAAGTATAAGCCAAATCA
Found at i:2162632 original size:21 final size:21
Alignment explanation
Indices: 2162603--2162655 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2162593 ATTCTGACTA
2162603 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
2162624 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
2162645 TCGCAATGCGA
1 TCGCATTGCGA
2162656 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:2162670 original size:20 final size:20
Alignment explanation
Indices: 2162645--2162798 Score: 218
Period size: 20 Copynumber: 7.7 Consensus size: 20
2162635 TTTTCCTAAT
2162645 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
2162665 TCGCAACGCGAATTTGGAAA
1 TCGCAATGCGAATACGTAAA
*
2162685 TTCGCAATGCGATTACGTAAA
1 -TCGCAATGCGAATACGTAAA
2162706 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
2162726 TTGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
2162746 TCGTAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
2162766 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
*
2162786 TCGCAACGCGAAT
1 TCGCAATGCGAAT
2162799 CTGACTATCA
Statistics
Matches: 117, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
20 102 0.87
21 15 0.13
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2162848 original size:20 final size:20
Alignment explanation
Indices: 2162785--2162851 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
2162775 GAATATGTAA
* *
2162785 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGATTCTGACT
*
2162805 ATCACAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
2162825 ATCGCAACGATATTCTGACT
1 ATCGCAACGAGATTCTGACT
2162845 ATCGCAA
1 ATCGCAA
2162852 TACTGAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:2163720 original size:24 final size:24
Alignment explanation
Indices: 2163693--2163746 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2163683 GTATTCGAAA
*
2163693 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGCCAATACCCGGAC
* *
2163717 TTTGATCTTGGCCAATACTCGGAT
1 TTTGATCTTGGCCAATACCCGGAC
2163741 TTTGAT
1 TTTGAT
2163747 AATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGGCCAATACCCGGAC
Found at i:2166217 original size:20 final size:20
Alignment explanation
Indices: 2166160--2166268 Score: 140
Period size: 20 Copynumber: 5.7 Consensus size: 20
2166150 GACATTCATT
2166160 TGACTATCGCAACGCGG-AA
1 TGACTATCGCAACGCGGAAA
*
2166179 --A-T-TCACAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
*
2166195 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
*
2166215 TGACTATCGCAACGCGGAAT
1 TGACTATCGCAACGCGGAAA
2166235 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
2166255 TGACTATCGCAACG
1 TGACTATCGCAACG
2166269 AGAGAATCGC
Statistics
Matches: 77, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
14 1 0.01
15 9 0.12
16 2 0.03
17 1 0.01
18 1 0.01
19 1 0.01
20 59 0.77
21 3 0.04
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:2166290 original size:33 final size:33
Alignment explanation
Indices: 2166240--2166335 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
2166230 GGAATTGACT
* **
2166240 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
2166274 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2166307 ATCGGAATGCGAAAATGAAAATTGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
2166336 CGAATTTAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.55
34 25 0.45
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2166408 original size:33 final size:34
Alignment explanation
Indices: 2166355--2166445 Score: 121
Period size: 33 Copynumber: 2.7 Consensus size: 34
2166345 TTTCGTGTTA
*
2166355 CGATTTTCATTTTTGCATTGCGATTCTCTCGTTG
1 CGATTTTCATTTTCGCATTGCGATTCTCTCGTTG
*
2166389 CGATTTTTA-TTTCGCATTGCGATTCTCTCGTTG
1 CGATTTTCATTTTCGCATTGCGATTCTCTCGTTG
** * *
2166422 CGATAGTCATTTCCGCGTTGCGAT
1 CGATTTTCATTTTCGCATTGCGAT
2166446 AGTCTGTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
33 29 0.59
34 20 0.41
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (34 bp):
CGATTTTCATTTTCGCATTGCGATTCTCTCGTTG
Found at i:2166570 original size:14 final size:14
Alignment explanation
Indices: 2166551--2166587 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2166541 TATCAATTAA
2166551 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2166565 ACAAATCATCTTTT
1 ACAAATCAACATTT
2166579 ACAAATCAA
1 ACAAATCAA
2166588 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2168020 original size:21 final size:21
Alignment explanation
Indices: 2167994--2168068 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
2167984 CGATGACAGT
2167994 GCCTCTTGAACGGTGGGAGGG
1 GCCTCTTGAACGGTGGGAGGG
* * **
2168015 GACTCTTG-AGGGATGATAGGG
1 GCCTCTTGAACGG-TGGGAGGG
* * *
2168036 GCCTCTTGAACGATAGGAGAG
1 GCCTCTTGAACGGTGGGAGGG
2168057 GCCTCTTGAACG
1 GCCTCTTGAACG
2168069 ATGACAGGTG
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
20 3 0.07
21 36 0.88
22 2 0.05
ACGTcount: A:0.21, C:0.19, G:0.39, T:0.21
Consensus pattern (21 bp):
GCCTCTTGAACGGTGGGAGGG
Found at i:2168072 original size:42 final size:41
Alignment explanation
Indices: 2167975--2168076 Score: 114
Period size: 42 Copynumber: 2.5 Consensus size: 41
2167965 TTGGGAGGGA
* * * * *
2167975 CCTCTTCAACGATGACAGTGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGACAGGGCCTCTTGAACGATAGGAGAGG
* ** *
2168016 ACTCTTGAGGGATGATAGGGGCCTCTTGAACGATAGGAGAGG
1 CCTCTTGAACGATGACA-GGGCCTCTTGAACGATAGGAGAGG
2168058 CCTCTTGAACGATGACAGG
1 CCTCTTGAACGATGACAGG
2168077 TGAGTCGGGC
Statistics
Matches: 47, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
41 14 0.30
42 33 0.70
ACGTcount: A:0.24, C:0.21, G:0.34, T:0.22
Consensus pattern (41 bp):
CCTCTTGAACGATGACAGGGCCTCTTGAACGATAGGAGAGG
Found at i:2168578 original size:20 final size:20
Alignment explanation
Indices: 2168555--2168681 Score: 164
Period size: 20 Copynumber: 6.3 Consensus size: 20
2168545 GAAACTTAAA
2168555 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
2168575 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
2168595 TTCACAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
2168615 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
2168635 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
** **
2168655 ATCGCAATACGAATTTGACT
1 ATCGCAACGCGAAAATGACT
2168675 ATCGCAA
1 ATCGCAA
2168682 TGAGAGAATC
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 99 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:2168753 original size:20 final size:20
Alignment explanation
Indices: 2168728--2168869 Score: 158
Period size: 20 Copynumber: 7.5 Consensus size: 20
2168718 AATTCTTTCG
*
2168728 TTGCGATAGTTATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
2168748 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
*
2168768 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
2168788 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
**
2168802 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
2168821 TTGCGATAGTCATTTT-GCG
1 TTGCGATAGTCATTTTCGCA
2168840 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
2168860 TTGCGATAGT
1 TTGCGATAGT
2168870 AAACTATTCT
Statistics
Matches: 104, Mismatches: 8, Indels: 20
0.79 0.06 0.15
Matches are distributed among these distances:
14 7 0.07
16 6 0.06
17 4 0.04
18 1 0.01
19 28 0.27
20 58 0.56
ACGTcount: A:0.17, C:0.16, G:0.23, T:0.44
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:2168826 original size:19 final size:20
Alignment explanation
Indices: 2168814--2168869 Score: 96
Period size: 19 Copynumber: 2.9 Consensus size: 20
2168804 GCGATTTTCA
2168814 TTTCGCATTGCGATAGTCAT
1 TTTCGCATTGCGATAGTCAT
*
2168834 TTT-GCGTTGCGATAGTCAT
1 TTTCGCATTGCGATAGTCAT
2168853 TTTCGCATTGCGATAGT
1 TTTCGCATTGCGATAGT
2168870 AAACTATTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (20 bp):
TTTCGCATTGCGATAGTCAT
Found at i:2170776 original size:20 final size:20
Alignment explanation
Indices: 2170753--2170841 Score: 90
Period size: 20 Copynumber: 4.5 Consensus size: 20
2170743 CTGAAACTTT
2170753 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
2170773 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** * **
2170793 CTATCGCAACGCGAATTTGA
1 AAATCGCAACACGAAAATGA
** *
2170813 CTATCGCAACGCG-AAATGA
1 AAATCGCAACACGAAAATGA
*
2170832 AAATTGCAAC
1 AAATCGCAAC
2170842 GACAGAATCG
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
19 11 0.19
20 48 0.81
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.16
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:2171212 original size:22 final size:22
Alignment explanation
Indices: 2171187--2171240 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2171177 ATGATTTCTC
2171187 CGGAGAT-GGAGACTGATATCGT
1 CGGAGATGGGA-ACTGATATCGT
*
2171209 CGGAGATGGGAACTGATTTCGT
1 CGGAGATGGGAACTGATATCGT
*
2171231 CAGAGATGGG
1 CGGAGATGGG
2171241 GATGGATGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.26, C:0.13, G:0.39, T:0.22
Consensus pattern (22 bp):
CGGAGATGGGAACTGATATCGT
Found at i:2171461 original size:20 final size:20
Alignment explanation
Indices: 2171438--2171533 Score: 156
Period size: 20 Copynumber: 4.8 Consensus size: 20
2171428 CGATAGTCAG
*
2171438 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
2171458 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
2171478 ATTCACATTGCGATTTTCGT
1 ATTCGCATTGCGATTTACGT
2171498 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
2171518 AATCGCATTGCGATTT
1 ATTCGCATTGCGATTT
2171534 TGCGATTTTC
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:2171558 original size:49 final size:48
Alignment explanation
Indices: 2171485--2171579 Score: 145
Period size: 49 Copynumber: 2.0 Consensus size: 48
2171475 CGTATTCACA
**
2171485 TTGCGATTTTCGTATTCGCATTGCGATTTACGTAATCGCATTGCGATT
1 TTGCGATTTTCAAATTCGCATTGCGATTTACGTAATCGCATTGCGATT
* *
2171533 TTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCATTGCGA
1 TTGCGATTTT-CAAATTCGCATTGCGATTTACGTAATCGCATTGCGA
2171580 ATTAAGAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 10 0.24
49 32 0.76
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (48 bp):
TTGCGATTTTCAAATTCGCATTGCGATTTACGTAATCGCATTGCGATT
Found at i:2171600 original size:21 final size:21
Alignment explanation
Indices: 2171576--2171621 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2171566 TATTCGCATT
2171576 GCGAATTAAGAAAATCGCAAC
1 GCGAATTAAGAAAATCGCAAC
** *
2171597 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAAGAAAATCGCAAC
2171618 GCGA
1 GCGA
2171622 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTAAGAAAATCGCAAC
Found at i:2174255 original size:12 final size:13
Alignment explanation
Indices: 2174233--2174262 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2174223 AGAAAGGTCA
2174233 AAAAAGTTTTTTT
1 AAAAAGTTTTTTT
2174246 AAAAAG-TTTTTT
1 AAAAAGTTTTTTT
2174258 AAAAA
1 AAAAA
2174263 AATTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (13 bp):
AAAAAGTTTTTTT
Found at i:2174263 original size:13 final size:13
Alignment explanation
Indices: 2174232--2174263 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2174222 TAGAAAGGTC
2174232 AAAAAAGTTTTTT
1 AAAAAAGTTTTTT
*
2174245 TAAAAAGTTTTTT
1 AAAAAAGTTTTTT
2174258 AAAAAA
1 AAAAAA
2174264 ATTAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (13 bp):
AAAAAAGTTTTTT
Found at i:2174903 original size:21 final size:21
Alignment explanation
Indices: 2174877--2174938 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
2174867 TTGGAACTGA
2174877 AAAATAAG-A-AAAAT-AAAT
1 AAAATAAGAATAAAATAAAAT
2174895 -AAAT--GAATAAAATAAAAT
1 AAAATAAGAATAAAATAAAAT
2174913 AAAATAAGAATAAAATAAAAT
1 AAAATAAGAATAAAATAAAAT
2174934 AAAAT
1 AAAAT
2174939 GGAATATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
15 1 0.03
16 1 0.03
17 9 0.24
18 4 0.11
19 4 0.11
21 19 0.50
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (21 bp):
AAAATAAGAATAAAATAAAAT
Found at i:2174910 original size:5 final size:5
Alignment explanation
Indices: 2174900--2174938 Score: 69
Period size: 5 Copynumber: 7.6 Consensus size: 5
2174890 TAAATAAATG
2174900 AATAA AATAA AATAA AATAA GAATAA AATAA AATAA AAT
1 AATAA AATAA AATAA AATAA -AATAA AATAA AATAA AAT
2174939 GGAATATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 28 0.85
6 5 0.15
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:2174926 original size:16 final size:15
Alignment explanation
Indices: 2174900--2174938 Score: 69
Period size: 16 Copynumber: 2.5 Consensus size: 15
2174890 TAAATAAATG
2174900 AATAAAATAAAATAA
1 AATAAAATAAAATAA
2174915 AATAAGAATAAAATAA
1 AATAA-AATAAAATAA
2174931 AATAAAAT
1 AATAAAAT
2174939 GGAATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AATAAAATAAAATAA
Found at i:2174944 original size:10 final size:10
Alignment explanation
Indices: 2174886--2174944 Score: 61
Period size: 10 Copynumber: 6.1 Consensus size: 10
2174876 AAAAATAAGA
2174886 AAAATA-AAT
1 AAAATAGAAT
2174895 -AAAT-GAAT
1 AAAATAGAAT
*
2174903 AAAATAAAAT
1 AAAATAGAAT
2174913 AAAATAAGAAT
1 AAAAT-AGAAT
*
2174924 AAAATAAAAT
1 AAAATAGAAT
*
2174934 AAAATGGAAT
1 AAAATAGAAT
2174944 A
1 A
2174945 TAAAATTCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
8 7 0.17
9 4 0.10
10 21 0.51
11 9 0.22
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (10 bp):
AAAATAGAAT
Found at i:2175000 original size:14 final size:14
Alignment explanation
Indices: 2174983--2175014 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2174973 ATATATTTTG
2174983 AAAAATATGTTTAA
1 AAAAATATGTTTAA
*
2174997 AAAAATATTTTTAA
1 AAAAATATGTTTAA
2175011 AAAA
1 AAAA
2175015 CTATATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (14 bp):
AAAAATATGTTTAA
Found at i:2175128 original size:36 final size:36
Alignment explanation
Indices: 2175043--2175214 Score: 106
Period size: 36 Copynumber: 4.6 Consensus size: 36
2175033 TTCAAAATTA
*
2175043 TTTTAAAAAT-TATTATTATATTTTTCAAAAACGTG
1 TTTTAAAAATATATTATTATATTTTCCAAAAACGTG
* * *
2175078 TTTTCAAAATTATATTATT-TGTTTTCCAAAATCGAT-
1 TTTT-AAAAATATATTATTATATTTTCCAAAAACG-TG
* **
2175114 TTTTAAAAACTATA-TATTATATACGTTTTCAAAAATATG
1 TTTTAAAAA-TATATTATTATAT---TTTCCAAAAACGTG
*
2175153 TTTTCAAAACTATATATTATTATATGTTT-TAAAAACCGT-
1 TTTT-AAAA--ATATATTATTATAT-TTTCCAAAAA-CGTG
2175192 TTTCTAAAAAT-TATATATTATAT
1 TTT-TAAAAATATAT-TATTATAT
2175215 GTTTTTCAAA
Statistics
Matches: 108, Mismatches: 13, Indels: 30
0.72 0.09 0.20
Matches are distributed among these distances:
35 12 0.11
36 30 0.28
37 18 0.17
38 1 0.01
39 24 0.22
40 10 0.09
41 4 0.04
42 9 0.08
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.48
Consensus pattern (36 bp):
TTTTAAAAATATATTATTATATTTTCCAAAAACGTG
Found at i:2175233 original size:38 final size:36
Alignment explanation
Indices: 2174987--2175251 Score: 182
Period size: 39 Copynumber: 7.1 Consensus size: 36
2174977 ATTTTGAAAA
** *
2174987 ATATGTTTAAAAAAATATTTTTAAAAAACTATATTATAT
1 ATATGTTTTCAAAAATATTTTT-AAAAATTATA-TAT-T
** *
2175026 ATACATTTTCAAAATTA-TTTTAAAAATTAT-TATT
1 ATATGTTTTCAAAAATATTTTTAAAAATTATATATT
** *
2175060 ATAT-TTTTCAAAAACGTGTTTTCAAAA-T-TATATT
1 ATATGTTTTCAAAAATAT-TTTTAAAAATTATATATT
* * *
2175094 ATTTGTTTTCCAAAATCGATTTTTAAAAACTATATATT
1 ATATGTTTTCAAAAAT--ATTTTTAAAAATTATATATT
*
2175132 ATATACGTTTTCAAAAATATGTTTTCAAAACTATATATTATT
1 ATAT--GTTTTCAAAAATAT-TTTT-AAAAAT-TATA-TATT
**
2175174 ATATGTTTT-AAAAACCGTTTTCTAAAAATTATATATT
1 ATATGTTTTCAAAAA-TATTTT-TAAAAATTATATATT
* *
2175211 ATATGTTTTTCAAAAATATTTTCAAAACTATACTATATT
1 ATATG-TTTTCAAAAATATTTTTAAAAAT-TA-TATATT
2175250 AT
1 AT
2175252 TATATATACT
Statistics
Matches: 179, Mismatches: 27, Indels: 40
0.73 0.11 0.16
Matches are distributed among these distances:
33 10 0.06
34 12 0.07
35 20 0.11
36 8 0.04
37 24 0.13
38 29 0.16
39 42 0.23
40 22 0.12
41 4 0.02
42 8 0.04
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (36 bp):
ATATGTTTTCAAAAATATTTTTAAAAATTATATATT
Found at i:2179961 original size:2 final size:2
Alignment explanation
Indices: 2179954--2179980 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2179944 TTTTCAAACT
2179954 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2179981 TAAAGACCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2180359 original size:2 final size:2
Alignment explanation
Indices: 2180352--2180387 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2180342 TTAATTAACC
*
2180352 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2180388 CTAAGCACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2188607 original size:17 final size:17
Alignment explanation
Indices: 2188574--2188607 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2188564 TTGAATATTT
* *
2188574 TGGATTGTTTGATTTTG
1 TGGATTGTTAGACTTTG
2188591 TGGATTGTTAGACTTTG
1 TGGATTGTTAGACTTTG
2188608 GATTTGTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.29, T:0.53
Consensus pattern (17 bp):
TGGATTGTTAGACTTTG
Found at i:2190386 original size:2 final size:2
Alignment explanation
Indices: 2190381--2190426 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
2190371 TAAGAGAGTA
*
2190381 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2190423 AT AT
1 AT AT
2190427 GGCGTTTAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2190800 original size:19 final size:19
Alignment explanation
Indices: 2190761--2190797 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
2190751 GATTATCGTC
2190761 GTCTCTCTAATTTTTTCTT
1 GTCTCTCTAATTTTTTCTT
2190780 GTCTCTCT-ATTTTTTCTT
1 GTCTCTCTAATTTTTTCTT
2190798 TGTGCCTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.08, C:0.22, G:0.05, T:0.65
Consensus pattern (19 bp):
GTCTCTCTAATTTTTTCTT
Found at i:2192325 original size:29 final size:28
Alignment explanation
Indices: 2192292--2192533 Score: 115
Period size: 29 Copynumber: 8.4 Consensus size: 28
2192282 AGAAATGTCA
* *
2192292 TTATTGTAATTTTTATGAAGTTTTGTATT
1 TTATTGTAATTTATA-AAAGTTTTGTATT
* *
2192321 TTATTGTAATTTATAAAATATTTTGTACT
1 TTATTGTAATTTATAAAA-GTTTTGTATT
*
2192350 TTATTGTAAATTCCA-AAAAGTTTTGTATT
1 TTATTGT-AATT-TATAAAAGTTTTGTATT
* * *
2192379 TTACTATAAATTCCA-AAAAG--TTGTCA-T
1 TTATTGT-AATT-TATAAAAGTTTTGT-ATT
* **
2192406 TTATTGTAAATTCCA-AAAAGTTTTGTCCT
1 TTATTGT-AATT-TATAAAAGTTTTGTATT
* * *
2192435 TTATTGTAAATTACAATTAGTTTTGT-TCT
1 TTATTGTAATTTATAA-AAGTTTTGTAT-T
* **
2192464 TTATTGTAAATTTCA-AAAAGTTTTATCCT
1 TTATTGT-AATTT-ATAAAAGTTTTGTATT
**
2192493 TTATTGTAAATTTCA-AAAAGTTTTGCCTT
1 TTATTGT-AATTT-ATAAAAGTTTTGTATT
2192522 TTATTGTAATTT
1 TTATTGTAATTT
2192534 TATTTTTTTA
Statistics
Matches: 177, Mismatches: 23, Indels: 27
0.78 0.10 0.12
Matches are distributed among these distances:
27 24 0.14
28 13 0.07
29 124 0.70
30 14 0.08
31 2 0.01
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.51
Consensus pattern (28 bp):
TTATTGTAATTTATAAAAGTTTTGTATT
Found at i:2192371 original size:58 final size:56
Alignment explanation
Indices: 2192309--2192530 Score: 207
Period size: 58 Copynumber: 3.9 Consensus size: 56
2192299 AATTTTTATG
* *
2192309 AAGTTTTGTATTTTATTGTAATTTATAAAATATTTTGTACTTTATTGTAAATTCCAAA
1 AAGTTTTGTACTTTATTGTAAATTA-AAAATATTTTGT-CTTTATTGTAAATTCCAAA
* * * * *
2192367 AAGTTTTGTATTTTACTATAAATTCCAAAA-A-GTTGTCATTTATTGTAAATTCCAAA
1 AAGTTTTGTACTTTATTGTAAATT-AAAAATATTTTGTC-TTTATTGTAAATTCCAAA
* * * *
2192423 AAGTTTTGTCCTTTATTGTAAATTACAATTAGTTTTGTTCTTTATTGTAAATTTCAAA
1 AAGTTTTGTACTTTATTGTAAATTAAAAATA-TTTTG-TCTTTATTGTAAATTCCAAA
* * * *
2192481 AAGTTTTATCCTTTATTGTAAATTTCAAAAA-GTTTTGCCTTTTATTGTAA
1 AAGTTTTGTACTTTATTGTAAA-TT-AAAAATATTTTGTC-TTTATTGTAA
2192531 TTTTATTTTT
Statistics
Matches: 136, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
55 3 0.02
56 43 0.32
57 2 0.01
58 81 0.60
59 4 0.03
60 3 0.02
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (56 bp):
AAGTTTTGTACTTTATTGTAAATTAAAAATATTTTGTCTTTATTGTAAATTCCAAA
Found at i:2192503 original size:114 final size:114
Alignment explanation
Indices: 2192309--2192514 Score: 279
Period size: 114 Copynumber: 1.8 Consensus size: 114
2192299 AATTTTTATG
* *
2192309 AAGTTTTGTATTTTATTGTAATTTATAAAATATTTTGTACTTTATTGTAAATTCCAAAAAGTTTT
1 AAGTTTTGTACTTTATTGTAAATTATAAAATATTTTGTACTTTATTGTAAATTCCAAAAAGTTTT
* *
2192374 GTATTTTACTATAAATTCCAAAAAGTTGTCATTTATTGTAAATTCCAAA
66 ATACTTTACTATAAATTCCAAAAAGTTGTCATTTATTGTAAATTCCAAA
* * * * *
2192423 AAGTTTTGTCCTTTATTGTAAATTA-CAATTAGTTTTGTTCTTTATTGTAAATTTCAAAAAGTTT
1 AAGTTTTGTACTTTATTGTAAATTATAAAATA-TTTTGTACTTTATTGTAAATTCCAAAAAGTTT
* * * *
2192487 TATCCTTTATTGTAAATTTCAAAAAGTT
65 TATACTTTACTATAAATTCCAAAAAGTT
2192515 TTGCCTTTTA
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
113 4 0.05
114 74 0.95
ACGTcount: A:0.34, C:0.08, G:0.09, T:0.49
Consensus pattern (114 bp):
AAGTTTTGTACTTTATTGTAAATTATAAAATATTTTGTACTTTATTGTAAATTCCAAAAAGTTTT
ATACTTTACTATAAATTCCAAAAAGTTGTCATTTATTGTAAATTCCAAA
Found at i:2202746 original size:21 final size:21
Alignment explanation
Indices: 2202722--2202761 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2202712 GCCATATAAA
2202722 ATATGTACC-GAAAGACCTCAT
1 ATATGT-CCTGAAAGACCTCAT
*
2202743 ATATGTCCTGAAGGACCTC
1 ATATGTCCTGAAAGACCTC
2202762 GTAGAACCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (21 bp):
ATATGTCCTGAAAGACCTCAT
Found at i:2206237 original size:14 final size:14
Alignment explanation
Indices: 2206215--2206256 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
2206205 AATAATATTT
2206215 ATATATTTCAAAAA
1 ATATATTTCAAAAA
*
2206229 ATATGTTTCAAAAA
1 ATATATTTCAAAAA
* *
2206243 ATATTTTTTAAAAA
1 ATATATTTCAAAAA
2206257 GCTATATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (14 bp):
ATATATTTCAAAAA
Found at i:2206271 original size:36 final size:35
Alignment explanation
Indices: 2206229--2206446 Score: 128
Period size: 36 Copynumber: 6.0 Consensus size: 35
2206219 ATTTCAAAAA
2206229 ATATGTTTCAAAAAATATTTTTTAAAAAGCTATATT
1 ATATGTTTCAAAAAATATTTTTTAAAAA-CTATATT
**
2206265 ATATGTTTCCAAAAACCA--TTTTAAAAACTATATATT
1 ATATGTTT-CAAAAAATATTTTTTAAAAAC--TATATT
* *
2206301 AAATGTTTTC-AAAAATATTTTTTTTAAAACTATATTAT
1 ATATG-TTTCAAAAAATA-TTTTTTAAAAACTATA-T-T
2206339 ATATACGTTTTC-AAAAATA--TTTTAAAAACTATATATT
1 ATAT--G-TTTCAAAAAATATTTTTTAAAAAC--TATATT
* * * *
2206376 ATATTTTTTTC-AAAAATGTGTTTTCAAAACTATATT
1 ATA--TGTTTCAAAAAATATTTTTTAAAAACTATATT
* * *
2206412 ATATGTTTTCCAAAACTGA-ATTTTAAAAACTATAT
1 ATATG-TTTCAAAAAAT-ATTTTTTAAAAACTATAT
2206447 ATTATATACG
Statistics
Matches: 146, Mismatches: 16, Indels: 40
0.72 0.08 0.20
Matches are distributed among these distances:
34 2 0.01
35 18 0.12
36 61 0.42
37 24 0.16
38 23 0.16
39 5 0.03
40 13 0.09
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (35 bp):
ATATGTTTCAAAAAATATTTTTTAAAAACTATATT
Found at i:2206464 original size:75 final size:73
Alignment explanation
Indices: 2206229--2206465 Score: 270
Period size: 75 Copynumber: 3.2 Consensus size: 73
2206219 ATTTCAAAAA
*
2206229 ATATG-TTTCAAAAAATATTTTTTAAAAAGCTATATTATATG-TTTCCAAAAACCATTTTAAAAA
1 ATATGTTTTC-AAAAATATTTTTTAAAAA-CTATATTATATGTTTTCC-AAAACTATTTTAAAAA
2206292 CTATATATTA-
63 CTATATATTAT
* *
2206302 A-ATGTTTTCAAAAATATTTTTTTTAAAACTATATTATATATACGTTTT-CAAAAATATTTTAAA
1 ATATGTTTTCAAAAATA-TTTTTTAAAAACTATA-T-TATAT--GTTTTCCAAAACTATTTTAAA
2206365 AACTATATATTAT
61 AACTATATATTAT
* * * *
2206378 AT-TTTTTTCAAAAATGTGTTTTCAAAACTATATTATATGTTTTCCAAAACTGAATTTTAAAAAC
1 ATATGTTTTCAAAAATATTTTTTAAAAACTATATTATATGTTTTCCAAAACT--ATTTTAAAAAC
2206442 TATATATTAT
64 TATATATTAT
*
2206452 ATACGTTTTCAAAA
1 ATATGTTTTCAAAA
2206466 CTATATATTA
Statistics
Matches: 141, Mismatches: 10, Indels: 24
0.81 0.06 0.14
Matches are distributed among these distances:
71 5 0.04
72 21 0.15
73 21 0.15
74 29 0.21
75 47 0.33
76 15 0.11
77 3 0.02
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (73 bp):
ATATGTTTTCAAAAATATTTTTTAAAAACTATATTATATGTTTTCCAAAACTATTTTAAAAACTA
TATATTAT
Found at i:2206466 original size:25 final size:25
Alignment explanation
Indices: 2206432--2206528 Score: 185
Period size: 25 Copynumber: 3.9 Consensus size: 25
2206422 CAAAACTGAA
*
2206432 TTTTAAAAACTATATATTATATACG
1 TTTTCAAAACTATATATTATATACG
2206457 TTTTCAAAACTATATATTATATACG
1 TTTTCAAAACTATATATTATATACG
2206482 TTTTCAAAACTATATATTATATACG
1 TTTTCAAAACTATATATTATATACG
2206507 TTTTCAAAACTATATATTATAT
1 TTTTCAAAACTATATATTATAT
2206529 GTTTTAAAAT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
25 71 1.00
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.45
Consensus pattern (25 bp):
TTTTCAAAACTATATATTATATACG
Found at i:2210215 original size:6 final size:6
Alignment explanation
Indices: 2210204--2210234 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2210194 TGCACTCTAA
2210204 CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT C
1 CCCTCT CCCTCT CCCTCT CCCTCT CCCTCT C
2210235 TTTATAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CCCTCT
Found at i:2214886 original size:21 final size:21
Alignment explanation
Indices: 2214857--2214897 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2214847 CGTAGTACAT
* *
2214857 AGGTTCTTCGGGATATAGATG
1 AGGTACTTCGGGACATAGATG
2214878 AGGTACTTCGGGACATAGAT
1 AGGTACTTCGGGACATAGAT
2214898 TTCAAATGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.32, T:0.29
Consensus pattern (21 bp):
AGGTACTTCGGGACATAGATG
Found at i:2216154 original size:19 final size:19
Alignment explanation
Indices: 2216130--2216182 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
2216120 GAATGCAATT
2216130 AGTGCATCGATGCATGAAG
1 AGTGCATCGATGCATGAAG
*
2216149 AGTGCATTGATGCATGAAG
1 AGTGCATCGATGCATGAAG
*
2216168 AGTGCTTCGAT-CATG
1 AGTGCATCGATGCATG
2216183 CATCAATGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
18 4 0.13
19 27 0.87
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.26
Consensus pattern (19 bp):
AGTGCATCGATGCATGAAG
Found at i:2216860 original size:21 final size:21
Alignment explanation
Indices: 2216836--2216892 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
2216826 GGGATTATAG
2216836 TGGTCCTTCGGGACATATCAA
1 TGGTCCTTCGGGACATATCAA
* *
2216857 TGGTCATTCGGGACATATCAG
1 TGGTCCTTCGGGACATATCAA
*
2216878 TAGTCCTTCGGGACA
1 TGGTCCTTCGGGACA
2216893 AATATTTAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (21 bp):
TGGTCCTTCGGGACATATCAA
Found at i:2219320 original size:2 final size:2
Alignment explanation
Indices: 2219313--2219343 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2219303 TGATTTATGA
2219313 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2219344 ATGGAATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2222259 original size:22 final size:21
Alignment explanation
Indices: 2222210--2222260 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
2222200 TACATATATG
2222210 TGATATGTGATAGAAGAAAAA
1 TGATATGTGATAGAAGAAAAA
* * *
2222231 TATATATGTGATTATAAGAGAAA
1 T-GATATGTGA-TAGAAGAAAAA
2222254 TGATATG
1 TGATATG
2222261 AATACATGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 1 0.04
22 13 0.54
23 10 0.42
ACGTcount: A:0.47, C:0.00, G:0.22, T:0.31
Consensus pattern (21 bp):
TGATATGTGATAGAAGAAAAA
Found at i:2222404 original size:21 final size:21
Alignment explanation
Indices: 2222357--2222418 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
2222347 AGTTATATAG
**
2222357 GTCCTTCGGGACATAGTACACAA
1 GTCCTTCGGGACATAG-A-TGAA
*
2222380 GTCCTTCGGGATATAGATGAA
1 GTCCTTCGGGACATAGATGAA
2222401 GTCCTTCGGGACATAGAT
1 GTCCTTCGGGACATAGAT
2222419 TTCACATGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 19 0.54
22 1 0.03
23 15 0.43
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
GTCCTTCGGGACATAGATGAA
Found at i:2227808 original size:13 final size:13
Alignment explanation
Indices: 2227790--2227815 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2227780 ATATATAAAT
2227790 GTTAAATTATTAA
1 GTTAAATTATTAA
2227803 GTTAAATTATTAA
1 GTTAAATTATTAA
2227816 TAATTTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
GTTAAATTATTAA
Found at i:2229348 original size:143 final size:143
Alignment explanation
Indices: 2229103--2229381 Score: 558
Period size: 143 Copynumber: 2.0 Consensus size: 143
2229093 AGCTTCTAAT
2229103 TTCTTTTTGAGTTCAAGCCTTTTTGAGTTCAAATTTCAATATTATATTTCGAGTTTGAGTTGAAC
1 TTCTTTTTGAGTTCAAGCCTTTTTGAGTTCAAATTTCAATATTATATTTCGAGTTTGAGTTGAAC
2229168 TTGATAATTTTTAGCTTGTGAATTTGAGTTTAGTTGAACTTACTTTTAAAGTTTTCAAGTTCGAG
66 TTGATAATTTTTAGCTTGTGAATTTGAGTTTAGTTGAACTTACTTTTAAAGTTTTCAAGTTCGAG
2229233 TCGAGCGAGCTTC
131 TCGAGCGAGCTTC
2229246 TTCTTTTTGAGTTCAAGCCTTTTTGAGTTCAAATTTCAATATTATATTTCGAGTTTGAGTTGAAC
1 TTCTTTTTGAGTTCAAGCCTTTTTGAGTTCAAATTTCAATATTATATTTCGAGTTTGAGTTGAAC
2229311 TTGATAATTTTTAGCTTGTGAATTTGAGTTTAGTTGAACTTACTTTTAAAGTTTTCAAGTTCGAG
66 TTGATAATTTTTAGCTTGTGAATTTGAGTTTAGTTGAACTTACTTTTAAAGTTTTCAAGTTCGAG
2229376 TCGAGC
131 TCGAGC
2229382 TCAGCAATAC
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
143 136 1.00
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.46
Consensus pattern (143 bp):
TTCTTTTTGAGTTCAAGCCTTTTTGAGTTCAAATTTCAATATTATATTTCGAGTTTGAGTTGAAC
TTGATAATTTTTAGCTTGTGAATTTGAGTTTAGTTGAACTTACTTTTAAAGTTTTCAAGTTCGAG
TCGAGCGAGCTTC
Found at i:2230932 original size:121 final size:125
Alignment explanation
Indices: 2230710--2230956 Score: 466
Period size: 121 Copynumber: 2.0 Consensus size: 125
2230700 ACTCATCTAA
2230710 CAATCTTAAATATTTATAAAACTAAAAGAATTTTATATCGCATATAAATAAATTGTTTTTGACGC
1 CAATCTTAAATATTTATAAAACTAAAAGAATTTTATATCGCATATAAATAAATTGTTTTTGACGC
2230775 ATGTAACCCTTTCTCTTTCTTTTGTATAAGAACCGGGGTCTCGGGCTGACCC-TATTTTG
66 ATGTAACCCTTTCTCTTTCTTTTGTATAAGAACCGGGGTCTCGGGCTGACCCGTATTTTG
2230834 CAATC-TAAATATTTATAAAACTAAAAGAATTTTATATCGCATAT-AATAAATTG-TTTTGACGC
1 CAATCTTAAATATTTATAAAACTAAAAGAATTTTATATCGCATATAAATAAATTGTTTTTGACGC
2230896 ATGTAACCCTTTCTCTTTCTTTTGTATAAGAACCGGGGTCTCGGGCTGACCCGTATTTTG
66 ATGTAACCCTTTCTCTTTCTTTTGTATAAGAACCGGGGTCTCGGGCTGACCCGTATTTTG
2230956 C
1 C
2230957 TGCTTTCTTT
Statistics
Matches: 122, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
121 61 0.50
122 17 0.14
123 39 0.32
124 5 0.04
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Consensus pattern (125 bp):
CAATCTTAAATATTTATAAAACTAAAAGAATTTTATATCGCATATAAATAAATTGTTTTTGACGC
ATGTAACCCTTTCTCTTTCTTTTGTATAAGAACCGGGGTCTCGGGCTGACCCGTATTTTG
Found at i:2245241 original size:24 final size:24
Alignment explanation
Indices: 2245197--2245246 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2245187 ATAAAGAACC
*
2245197 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
2245221 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
2245245 AA
1 AA
2245247 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:2248895 original size:12 final size:11
Alignment explanation
Indices: 2248879--2248931 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
2248869 AAATCATATC
*
2248879 AAAAATTAAAT
1 AAAAATGAAAT
2248890 ACAAAATGAAAT
1 A-AAAATGAAAT
*
2248902 AAAAATAAAAAT
1 AAAAAT-GAAAT
*
2248914 AAAAATAAAAAT
1 AAAAAT-GAAAT
2248926 AAAAAT
1 AAAAAT
2248932 AAAAATAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
11 6 0.16
12 32 0.84
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (11 bp):
AAAAATGAAAT
Found at i:2248909 original size:6 final size:6
Alignment explanation
Indices: 2248898--2248940 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
2248888 ATACAAAATG
2248898 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A
2248941 GAAAAACTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:2253425 original size:24 final size:24
Alignment explanation
Indices: 2253381--2253430 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2253371 ATAAAGAACC
*
2253381 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
2253405 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
2253429 AA
1 AA
2253431 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:2261651 original size:21 final size:21
Alignment explanation
Indices: 2261627--2261668 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2261617 TTCTATAATG
* *
2261627 AATGGTCAATTTGAAAGATTA
1 AATGGCCAATTTGAAAAATTA
2261648 AATGGCCAATTTGAAAAATTA
1 AATGGCCAATTTGAAAAATTA
2261669 TTGAGCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (21 bp):
AATGGCCAATTTGAAAAATTA
Found at i:2267038 original size:21 final size:21
Alignment explanation
Indices: 2267001--2267042 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2266991 GTTCATCTCT
*
2267001 ATACATTTACCATTTACAAAA
1 ATACATTTAACATTTACAAAA
2267022 ATACATTTAAACA-TTACAAAA
1 ATACATTT-AACATTTACAAAA
2267043 CTTGTTCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (21 bp):
ATACATTTAACATTTACAAAA
Found at i:2267804 original size:63 final size:62
Alignment explanation
Indices: 2267689--2267808 Score: 163
Period size: 62 Copynumber: 1.9 Consensus size: 62
2267679 AACCTCGGCA
* *
2267689 ACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAAGTAT
1 ACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAAGTAT
* *
2267751 ACTGTCCATATGTCTCGAA-AGACATAGGTAATTA-TGTCCATATGTTCCGTAGAACATA
1 ACTGTCCATAGGTCCCGAAGA-ACATAGGTAA--ACTGTCCATATGTTCCGTAGAACATA
2267809 GGTAAACCCT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
61 1 0.02
62 26 0.51
63 23 0.45
64 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (62 bp):
ACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAAGTAT
Found at i:2267808 original size:32 final size:32
Alignment explanation
Indices: 2267689--2267813 Score: 125
Period size: 31 Copynumber: 4.0 Consensus size: 32
2267679 AACCTCGGCA
* * * *
2267689 ACTGTCCATAGGTCCCGAAGAACCTAGGTAA-
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
* *
2267720 ACTGTCCATATGTTCCTTAGAACATAAGT-AT
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
*
2267751 ACTGTCCATATG-TCTCG-AAAGACATAGGTAATT
1 ACTGTCCATATGTTC-CGTAGA-ACATAGGTAA-T
2267784 A-TGTCCATATGTTCCGTAGAACATAGGTAA
1 ACTGTCCATATGTTCCGTAGAACATAGGTAA
2267814 ACCCTCGACT
Statistics
Matches: 77, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
30 5 0.06
31 43 0.56
32 23 0.30
33 6 0.08
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (32 bp):
ACTGTCCATATGTTCCGTAGAACATAGGTAAT
Found at i:2268786 original size:21 final size:21
Alignment explanation
Indices: 2268749--2268805 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
2268739 TTTCTTTAGC
*
2268749 GGGTATCGATA-CCCCCCATA
1 GGGTATTGATACCCCCCCATA
2268769 GGGTATTGATACCCCCCCATA
1 GGGTATTGATACCCCCCCATA
2268790 GGGTATCTG-TACCCCC
1 GGGTAT-TGATACCCCC
2268806 TACATAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 10 0.29
21 22 0.65
22 2 0.06
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.23
Consensus pattern (21 bp):
GGGTATTGATACCCCCCCATA
Found at i:2278924 original size:133 final size:133
Alignment explanation
Indices: 2278681--2278978 Score: 447
Period size: 133 Copynumber: 2.2 Consensus size: 133
2278671 ACAATGAAGA
* * * *
2278681 TTTGCTCTCCACGGAAGAGTAGTTGAAGCAAATCGACATCGAATCTGATCTTCACGGAAGAGTAG
1 TTTGATCTCCACGGAAGAGTAGTGGAAGCAAATCAACATCGAATCTGATCTTCACAGAAGAGTAG
* * * *
2278746 TGAAGCCGATTCTTTTCAAGTAAATCCAGCCTTCACAAAAGAGTAGTGAAGCAGGAACAGACCAA
66 TGAAGCAGATTCTTTTCAAGCAAATCCAGCCTTCACAAAAGAGTAGTGAAGCAAGAACAAACCAA
2278811 AAG
131 AAG
* *
2278814 TTTTG-TCTCCACGGAAGAGTGGTGGAAGCAAATCAACATCTAATCTGATCTTCACAGAAGAGTA
1 -TTTGATCTCCACGGAAGAGTAGTGGAAGCAAATCAACATCGAATCTGATCTTCACAGAAGAGTA
* *
2278878 GTGAAGCAGATTCTTTTCAAGCAAATCCAGCCTTCACAAAAGAGTAGTGAAGCAAGATCAAATCA
65 GTGAAGCAGATTCTTTTCAAGCAAATCCAGCCTTCACAAAAGAGTAGTGAAGCAAGAACAAACCA
2278943 AAAG
130 AAAG
* *
2278947 TTCGATCTCCACGGAATAGTAGTGGAA-CAAAT
1 TTTGATCTCCACGGAAGAGTAGTGGAAGCAAAT
2278979 TTTTATCAAA
Statistics
Matches: 149, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
132 8 0.05
133 137 0.92
134 4 0.03
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.23
Consensus pattern (133 bp):
TTTGATCTCCACGGAAGAGTAGTGGAAGCAAATCAACATCGAATCTGATCTTCACAGAAGAGTAG
TGAAGCAGATTCTTTTCAAGCAAATCCAGCCTTCACAAAAGAGTAGTGAAGCAAGAACAAACCAA
AAG
Found at i:2282908 original size:98 final size:97
Alignment explanation
Indices: 2282737--2282993 Score: 295
Period size: 98 Copynumber: 2.6 Consensus size: 97
2282727 GTGATCGTAC
* * * * * * *
2282737 CGATACATTCTCGTATCAATACCTTGGAGAAATACTGGAATTTCATAAAATGTAAGTGTACTGGT
1 CGATACA-TCTCGTATCGATACCTTTGACACATACTGAAATTTCATAAAATGTAAGCGTACTGAT
* *
2282802 ACAATTACAAGTGTGTATCGGTACACCCAGTAT
65 ACAATTACAAGTGTGTATCGATACACCCAATAT
2282835 CGATACATCCTCGTATCGATACCTTTGACACATACTGAAATTTCATAAAATGTAAGCGTA-TCGA
1 CGATACAT-CTCGTATCGATACCTTTGACACATACTGAAATTTCATAAAATGTAAGCGTACT-GA
* * *
2282899 TACATTTACAGGTGTGTATCGATACACGCAATAT
64 TACAATTACAAGTGTGTATCGATACACCCAATAT
* * * * *
2282933 CAATACTAT-TAGTATTGGTACCTTTGACACATACT-AGAATTTCATAAAATGTAAGTGTACT
1 CGATAC-ATCTCGTATCGATACCTTTGACACATACTGA-AATTTCATAAAATGTAAGCGTACT
2282994 AGTACGTTTT
Statistics
Matches: 137, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
96 1 0.01
97 46 0.34
98 88 0.64
99 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (97 bp):
CGATACATCTCGTATCGATACCTTTGACACATACTGAAATTTCATAAAATGTAAGCGTACTGATA
CAATTACAAGTGTGTATCGATACACCCAATAT
Found at i:2284994 original size:211 final size:211
Alignment explanation
Indices: 2284623--2285044 Score: 774
Period size: 211 Copynumber: 2.0 Consensus size: 211
2284613 TATGTGTAAA
* *
2284623 AACCTAGAAACAAATATAATTTTTGAATAAATATAACTAAAAACAAAAAACCATAAAGGTTCAAT
1 AACCTAAAAACAAATATAATTTGTGAATAAATATAACTAAAAACAAAAAACCATAAAGGTTCAAT
2284688 CTAGATACAAAAAGCTAAAAAAATAATATTCAGATGAATAAGTTAAATGAAATTCGAACAATACC
66 CTAGATACAAAAAGCTAAAAAAATAATATTCAGATGAATAAGTTAAATGAAATTCGAACAATACC
*
2284753 TAGGAATAATGTGATGAGTATGCACGGTTCATTGTTCAGAGATGAAATCCCTTGAAATGCTTGCA
131 TAGGAATAATGTGATGAGTATGCACGGTTCATTGTTCAGAGATGAAATCCCTTGAAATCCTTGCA
2284818 AAAACCATGAAGGATT
196 AAAACCATGAAGGATT
2284834 AACCTAAAAACAAATATAATTTGTGAATAAAT-TAAACTAAAAACAAAAAACCATAAAGGTTCAA
1 AACCTAAAAACAAATATAATTTGTGAATAAATAT-AACTAAAAACAAAAAACCATAAAGGTTCAA
* * *
2284898 TCTAGATACAAAAAGGTAAAAAAGTAATATTCAGATGAATAAGTTAAATGAAATTCGAATAATAC
65 TCTAGATACAAAAAGCTAAAAAAATAATATTCAGATGAATAAGTTAAATGAAATTCGAACAATAC
2284963 CTAGGAATAATGTGATGAGTATGCACGGTTCATTGTTCAGAGATGAAATCCCTTGAAATCCTTGC
130 CTAGGAATAATGTGATGAGTATGCACGGTTCATTGTTCAGAGATGAAATCCCTTGAAATCCTTGC
2285028 AAAAACCATGAAGGATT
195 AAAAACCATGAAGGATT
2285045 TTTGTAGTTT
Statistics
Matches: 204, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
210 1 0.00
211 203 1.00
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (211 bp):
AACCTAAAAACAAATATAATTTGTGAATAAATATAACTAAAAACAAAAAACCATAAAGGTTCAAT
CTAGATACAAAAAGCTAAAAAAATAATATTCAGATGAATAAGTTAAATGAAATTCGAACAATACC
TAGGAATAATGTGATGAGTATGCACGGTTCATTGTTCAGAGATGAAATCCCTTGAAATCCTTGCA
AAAACCATGAAGGATT
Found at i:2289922 original size:16 final size:15
Alignment explanation
Indices: 2289901--2289939 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
2289891 ATAAAAACTA
2289901 ATATTTAATAAATATT
1 ATATTTAATAAA-ATT
*
2289917 ATATTTAATTAAATT
1 ATATTTAATAAAATT
2289932 AT-TTTAAT
1 ATATTTAAT
2289940 TTTTAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.27
15 5 0.23
16 11 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATATTTAATAAAATT
Found at i:2291755 original size:17 final size:17
Alignment explanation
Indices: 2291723--2291773 Score: 75
Period size: 18 Copynumber: 2.9 Consensus size: 17
2291713 ATAAAACGAA
*
2291723 TAAATAAATGATTTTGAT
1 TAAAAAAAT-ATTTTGAT
2291741 TAAAAAAATATTTTGAT
1 TAAAAAAATATTTTGAT
2291758 TAAAAAAAATATTTTG
1 T-AAAAAAATATTTTG
2291774 GGAGTCGTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 9 0.29
18 22 0.71
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (17 bp):
TAAAAAAATATTTTGAT
Found at i:2293698 original size:3 final size:3
Alignment explanation
Indices: 2293690--2293744 Score: 78
Period size: 3 Copynumber: 18.7 Consensus size: 3
2293680 ATTTACTATT
*
2293690 TAA TAA TAA TAA T-A TAA -CA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2293736 TTAA TAA TA
1 -TAA TAA TA
2293745 TAAGCAAATG
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 3 0.06
3 41 0.87
4 3 0.06
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2293730 original size:28 final size:28
Alignment explanation
Indices: 2293690--2293744 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
2293680 ATTTACTATT
2293690 TAATAATAATAAT-ATAACATAATAATAA
1 TAATAATAATAATAATAA-ATAATAATAA
*
2293718 TAATAATAATAATAATAATTAATAATA
1 TAATAATAATAATAATAAATAATAATA
2293745 TAAGCAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (28 bp):
TAATAATAATAATAATAAATAATAATAA
Found at i:2294299 original size:124 final size:125
Alignment explanation
Indices: 2293978--2294517 Score: 683
Period size: 124 Copynumber: 4.5 Consensus size: 125
2293968 GTTGAACAAA
* * * *
2293978 TTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTTCTGGAAATGCTGATATTGA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTCTGGAAAAGTTGATACTGA
* * *
2294041 TCGATCTTCTTCTGTGATAGAATCA--AATAAAGGTTGAACAAGTTCTTCTCATTATGAAC
66 TCTATCTTCTTCTGTGATAGAGTCATGAA-AAAGGTTGAACAAGCTCTTCTCATTATGAAC
* * *
2294100 TTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTT-TTCTAGAAAAGTTGATGCTGA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTCTGGAAAAGTTGATACTGA
*
2294163 TCTATCTTCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
66 TCTATCTTCTTCTGTGATAGAGTCATGAAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
* *
2294223 TTCTTCTTCCTTCTTGAGATGAGTTCTTCTCATTATGAACTTTCTT-TGGAAAAGTTGATACTGG
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTCTGGAAAAGTTGATACTGA
* * *
2294287 TTTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
66 TCTATCTTCTTCTGTGATAGAGTCATGAAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
2294347 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTC-TCTGGAAAAGTTGAT-C---
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTCTGGAAAAGTTGATACTGA
** * * * * *
2294407 -C-A---TC--GAGTGAT-GAATTAAAGAAAAAGGTTGAACAAGTTATTCTCATTATGAAC
66 TCTATCTTCTTCTGTGATAG-AGTCATGAAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
* *
2294460 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC--ACTTCTGGAAATGTTGAT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTCTGGAAAAGTTGAT
2294518 CCATCAAGTG
Statistics
Matches: 378, Mismatches: 31, Indels: 28
0.86 0.07 0.06
Matches are distributed among these distances:
111 1 0.00
112 15 0.04
113 79 0.21
115 1 0.00
118 1 0.00
122 73 0.19
123 46 0.12
124 160 0.42
125 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (125 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTCTGGAAAAGTTGATACTGA
TCTATCTTCTTCTGTGATAGAGTCATGAAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
Done.